相关论文: Constructing minimal phylogenetic networks from so…

Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…

For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…

We consider the following natural graph cut problem called Critical Node Cut (CNC): Given a graph $G$ on $n$ vertices, and two positive integers $k$ and $x$, determine whether $G$ has a set of $k$ vertices whose removal leaves $G$ with at…

A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…

Dynamic networks are increasingly being usedd to model real world datasets. A challenging task in their analysis is to detect and characterize clusters. It is useful for analyzing real-world data such as detecting evolving communities in…

Network representations can help reveal the behavior of complex systems. Useful information can be derived from the network properties and invariants, such as components, clusters or cliques, as well as from their changes over time. The…

Recently, a framework for analyzing time series by constructing an associated complex network has attracted significant research interest. One of the advantages of the complex network method for studying time series is that complex network…

We present a generator of random networks where both the degree-dependent clustering coefficient and the degree distribution are tunable. Following the same philosophy as in the configuration model, the degree distribution and the…

We propose a general framework for modelling network data that is designed to describe aspects of non-exchangeable networks. Conditional on latent (unobserved) variables, the edges of the network are generated by their finite growth history…

Motivated by problems of uncertainty propagation and robust estimation we are interested in computing a polynomial sublevel set of fixed degree and minimum volume that contains a given semialgebraic set K. At this level of generality this…

In the vertex connectivity augmentation problem, we are given an undirected $n$-vertex graph $G$, a set of links $L \subseteq \binom{V(G)}{2} \setminus E(G)$, and integers $\lambda$ and $k$. The task is to insert at most $k$ links from $L$…

Latent variable models for network data extract a summary of the relational structure underlying an observed network. The simplest possible models subdivide nodes of the network into clusters; the probability of a link between any two nodes…

A connectivity function on a finite set $V$ is a symmetric submodular function $f \colon 2^V \to \mathbb{Z}$ with $f(\emptyset)=0$. We prove that finding a branch-decomposition of width at most $k$ for a connectivity function given by an…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…

In this article, we take a closer look at the reliability of large minimal networks constructed by repeated compositions of the simplest possible networks. For a given number of devices $n=2^m$ we define the set of all the possible…

Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…

We consider the parameterized complexity of the problem of tracking shortest s-t paths in graphs, motivated by applications in security and wireless networks. Given an undirected and unweighted graph with a source s and a destination t,…

We present a simple proof that finding a rank-$R$ canonical polyadic decomposition of a 3-dimensional tensor over a finite field $\mathbb{F}$ is fixed-parameter tractable with respect to $R$ and $\mathbb{F}$. We also show a nontrivial upper…